The Manchester City striker, whose proposed move to Sporting Lisbon collapsed last week, has suffered the consequences of his team's embarrassing goalless draw in Liechtenstein last weekend and is set to be replaced by Tony Cascarino, now playing in France for Marseille.
That result against the group's makeweights, which handed them their first point of the qualifying competition, was Charlton's worst in nine years at the Irish helm.
Charlton has never been a man to react impulsively to occasional failure, but is worried by Quinn's state of mind after the breakdown of his transfer. "His head is messed up over this and, of course, it is a concern for me because Niall has always been an important player for us," Charlton said.
Cascarino has had a very impressive first season with Marseille, scoring 38 goals in the French Second Division - he looked a far better scoring proposition than Quinn when substituting for him in the last half hour in Liechtenstein. There could also be another recall for the Motherwell marksman, Tommy Coyne.
Charlton may also make two midfield changes, with Portsmouth's Alan McLoughlin winning a rare chance in place of Southend United's Ronnie Whelan, and Ray Houghton, of Crystal Palace, returning for Bolton's Jason McAteer on the right, as the manager again goes into action without his injured captain Andy Townsend.
Charlton said: "We gave ourselves a big problem with that performance last week, and although the situation is slightly eased now [following Latvia's defeat of Northern Ireland], we have still got to get a good result against Austria to stay confident of qualifying."
There may be no better time to face Herbert Prohaska's Austrians, who are without the key defender Andreas Herzog and the Salzburg midfield pair, Peter Artner and Wolfgang Feiersinger. Defeat in Dublin would virtually end their hopes of qualifying, having already lost twice.Reuse content